Link to this post | posted 18 Jun, 2024 01:54
afreise	A phage with a genome >200 kbp.

Link to this post | posted 12 Jun, 2024 18:06
afreise	Hello! Curious as to whether anyone is working on jumbo phages, what protocols you use for annotation, and how you involve your students in this process. Cheers, Amanda

Link to this post | posted 24 Jan, 2024 01:00
afreise	thanks, Debbie! and thanks for the note about the preceding gene too!

Link to this post | posted 23 Jan, 2024 23:50

afreise

We are having a tricky time with the putative tail assembly chaperone for Singleton RomansRevenge. Its closest relatives are cluster AP phages. Most AP phages do not annotate a TAC, but several do (e.g, PureGlobe5). Please see the attached PPT for data collection. There is coding potential in the top reading frame on genemark for a potential new gene (RR_27), and the stop site looks like it would be 19980. Though the first putative TAC gene in RomansRevenge (gp26) is in the same pham as PureGlobe5's first TAC gene, there are significant sequence differences. I aligned them and looked for the slippery sequence in the same region I saw the shift in PureGlobe5, but I am not seeing any of the canonical slippery sequences in RomansRevenge_26. 257Kb

Link to this post | posted 22 Jan, 2024 17:38
afreise	The approved function list still lists the old evidence requirements (TmHmm, TOPCONS) for membrane proteins - could this be updated? https://docs.google.com/spreadsheets/d/e/2PACX-1vToasuRfxx_yfLa9ECFN4_6okwNI_5AJGWZ3NCy53Gz0QfoNrhAQ48HnBuSD1hsrY0zUTTn6EP3MGK_/pubhtml?gid=0&single=true

Link to this post | posted 26 Dec, 2023 21:00

afreise

Good news! VMWare Fusion version 13.5 contains a built-in approach to installing WIndows 11 ARM version. All you have to do is install VMWare and then when the wizard pops up, select 'Get Windows from Microsoft". It will auto-download the ARM version. I used it and then downloaded DNA Master using Kristen's update package successfully. Note: when you first boot Windows, you must click within the window and press a key within 5 seconds or it will time out. (more info: https://communities.vmware.com/t5/VMware-Fusion-Discussions/Windows-11-download-not-working/td-p/2992757)

Link to this post | posted 03 Jun, 2023 15:32
afreise	Hi Dan - could we get a new forum for Cluster FP phages?

Link to this post | posted 17 Mar, 2023 20:10
afreise	Ah! I should have tried the old off-and-on trick first (did it with DNA Master, but not the entire machine). That solved the problem. Thank you Debbie!

Link to this post | posted 16 Mar, 2023 23:51

afreise

Hello, I'm encountering some unexpected errors in DNA master. This is true for both old DNAM files I have previously successfully worked with, and a new one I made from the FASTA sequence. When I open the file, I get an error that says: "Field 'Path' must have a value." I'm able to work in the file from there, but when I add my notes to the documentation and parse, the feature table is coming up empty. Again, this is true using both new notes files and old ones that previously did work. Other times I try to open a file and get "Stream write error". In this case the file does not open at all. But if I try again, it does sometimes open the file. I have updated DNA Master and the problems persist. Any ideas on how to solve this?

Link to this post | posted 09 Feb, 2023 23:07
afreise	Hi Debbie et al., In the January 2023 faculty meeting you updated guidance on TMD prediction. As of now we are using just DeepTMHMM and looking for at least one TMD, about ~17-22aa long. My question is…how close does that "~" need to be? If DeepTMHMM predicts a TMD of 15 or 16aa, are those close enough? Or does it need to fall WITHIN 17-22aa long? Thanks, Amanda